How much does a FAIL grade in thesis credits affect PhD admission chances? I am doing an integrated BS-MS in Biological Science from an Indian university and currently am in the 6th (post-final!) year. In this MS part of the program, I am supposed to take a few grad level classes and mainly focus in research. I also need to pass 8 MS thesis courses (worth 3 credits each), in which my supervisor grades me on my research work that particular semester (I can take as many as 4 of them in one semester). The grade for this course is either S or X i.e. Satisfactory or Fail.

I took one of the 8 courses in the summer following my senior year. I worked very little and met my supervisor only 3 times in the term. As a result, I received the X grade in the thesis course. In the following semester (Fall), I took 3 MS thesis courses. My performance was better, I met him more often but according to him, it was not worth passing all 3 - he said it was only good enough to pass 1 of the 3 thesis courses. But since failing 3 thesis courses would have led to termination of my degree, he gave me pass grade for 2 of the 3 courses and cautioned me that another fail course would mean the end of the program for me. 

After this, my performance research-wise has been good, I have been more regular. My relationship with my supervisor has also improved, although it could be much better. I have received a pass grade in all the remaining thesis courses and retook the 2 I had failed. Since I had not made enough progress in the one year, I continued my work further until it reaches a publishable position. I am finishing my second year this summer (6th year overall) and the work seems to be coming to an end.

I applied to for PhD positions at US universities last fall. When I asked my supervisor for recommendation, he said - "Ya, I will write one for you, but it won't be a glorious recommendation. I will mention what you did, your performance in my course...". Anyway, the results came out, and it was not good (1 accept out of 9).

(hope this was enough of a background!)

My question is - How much does an X grade in thesis research course (2 such, in my case) affect my PhD application. Are these thesis credits looked at closely? Such X grades are rare in my department, so I don't know how bad the situation is. 

EDIT - I think this question is sufficiently different from others asking about a failed subject course. I am asking about failing thesis credits, which is different because a) these can be easily retaken and one can take as many as 4 of them in a semester and b) they directly corroborate with your research performance as opposed to normal courses.

I would be SINCERELY OBLIGED if someone could help me with this. It has been troubling me for months, and any answer towards this question/situation would be enormous for me!
To be successful in applying for PhD programmes, you need to demonstrate your ability to perform research.

Unfortunately, failing a thesis research course says rather the opposite to the admissions committee. By the sounds of it, your lukewarm recommendation letter from your supervisor will have done nothing to help matters either.

To improve your chances if you are planning to apply again, I would suggest trying to publish your work (you hint in your question that this may be possible) and, if you can, finding someone else who can write you a much stronger letter of recommendation.